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Hünten S, Kaller M, Drepper F, Oeljeklaus S, Bonfert T, Erhard F, Dueck A, Eichner N, Friedel CC, Meister G, Zimmer R, Warscheid B, Hermeking H. p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses. Mol Cell Proteomics 2015; 14:2609-29. [PMID: 26183718 DOI: 10.1074/mcp.m115.050237] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/20/2022] Open
Abstract
We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics (pulsed stable isotope labeling with amino acids in cell culture/pSILAC) in the colorectal cancer cell line SW480. This was combined with mRNA and noncoding RNA expression analyses by next generation sequencing (RNA-, miR-Seq). Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated proteins (542 up, 569 down), mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down) and lncRNAs (270 up, 123 down). Changes in protein and mRNA expression levels showed a positive correlation (r = 0.50, p < 0.0001). In total, we detected 133 direct p53 target genes that were differentially expressed and displayed p53 occupancy in the vicinity of their promoter. More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the down-regulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3'-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed up-regulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibits proliferation in SW480 cells. Furthermore, KLF12, HMGB1 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of KLF12, HMGB1 and CIT was detected in advanced stages of cancer. In conclusion, the integration of multiple omics methods allowed the comprehensive identification of direct and indirect effectors of p53 that provide new insights and leads into the mechanisms of p53-mediated tumor suppression.
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Affiliation(s)
- Sabine Hünten
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany
| | - Markus Kaller
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany
| | - Friedel Drepper
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Silke Oeljeklaus
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Bonfert
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Florian Erhard
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Anne Dueck
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Norbert Eichner
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Caroline C Friedel
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Gunter Meister
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Ralf Zimmer
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Bettina Warscheid
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; **Center for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany
| | - Heiko Hermeking
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany; §German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany; ¶German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany;
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Siemens H, Jackstadt R, Hünten S, Kaller M, Menssen A, Götz U, Hermeking H. miR-34 and SNAIL form a double-negative feedback loop to regulate epithelial-mesenchymal transitions. Cell Cycle 2011; 10:4256-71. [PMID: 22134354 DOI: 10.4161/cc.10.24.18552] [Citation(s) in RCA: 449] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recently, the inhibition of epithelial-mesenchymal-transition (EMT) by p53 has been described as a new mode of tumor suppression which presumably prevents metastasis. Here we report that activation of p53 down-regulates the EMT-inducing transcription factor SNAIL via induction of the miR-34a/b/c genes. Suppression of miR-34a/b/c caused up-regulation of SNAIL and cells displayed EMT markers and related features, as enhanced migration and invasion. Ectopic miR-34a induced mesenchymal-epithelial-transition (MET) and down-regulation of SNAIL, which was mediated by a conserved miR-34a/b/c seed-matching sequence in the SNAIL 3'-UTR. miR-34a also down-regulated SLUG and ZEB1, as well as the stemness factors BMI1, CD44, CD133, OLFM4 and c-MYC. Conversely, the transcription factors SNAIL and ZEB1 bound to E-boxes in the miR-34a/b/c promoters, thereby repressing miR-34a and miR-34b/c expression. Since ectopic miR-34a prevented TGF-β-induced EMT, the repression of miR-34 genes by SNAIL and related factors is part of the EMT program. In conclusion, the frequent inactivation of p53 and/or miR-34a/b/c found in cancer may shift the equilibrium of these reciprocal regulations towards the mesenchymal state and thereby lock cells in a metastatic state.
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Affiliation(s)
- Helge Siemens
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Munich, Germany
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Zawacka-Pankau J, Grinkevich VV, Hünten S, Nikulenkov F, Gluch A, Li H, Enge M, Kel A, Selivanova G. Inhibition of glycolytic enzymes mediated by pharmacologically activated p53: targeting Warburg effect to fight cancer. J Biol Chem 2011; 286:41600-41615. [PMID: 21862591 DOI: 10.1074/jbc.m111.240812] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Unique sensitivity of tumor cells to the inhibition of glycolysis is a good target for anticancer therapy. Here, we demonstrate that the pharmacologically activated tumor suppressor p53 mediates the inhibition of glycolytic enzymes in cancer cells in vitro and in vivo. We showed that p53 binds to the promoters of metabolic genes and represses their expression, including glucose transporters SLC2A12 (GLUT12) and SLC2A1 (GLUT1). Furthermore, p53-mediated repression of transcription factors c-Myc and HIF1α, key drivers of ATP-generating pathways in tumors, contributed to ATP production block. Inhibition of c-Myc by p53 mediated the ablation of several glycolytic genes in normoxia, whereas in hypoxia down-regulation of HIF1α contributed to this effect. We identified Sp1 as a transcription cofactor cooperating with p53 in the ablation of metabolic genes. Using different approaches, we demonstrated that glycolysis block contributes to the robust induction of apoptosis by p53 in cancer cells. Taken together, our data suggest that tumor-specific reinstatement of p53 function targets the "Achilles heel" of cancer cells (i.e. their dependence on glycolysis), which could contribute to the tumor-selective killing of cancer cells by pharmacologically activated p53.
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Affiliation(s)
- Joanna Zawacka-Pankau
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden; Department of Biotechnology, Division of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, 80-822 Gdansk, Poland.
| | - Vera V Grinkevich
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | - Sabine Hünten
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | - Fedor Nikulenkov
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | | | - Hai Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | - Martin Enge
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden
| | - Alexander Kel
- geneXplain GmbH, Am Exer 10b, D-38302 Wolfenbuettel, Germany
| | - Galina Selivanova
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Nobelsväg 16, Stockholm, SE 171 77, Sweden.
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